NEW YORK (GenomeWeb) – Appistry has launched a new software application called GenomePilot that provides preconfigured analysis tools and pipelines for clinical laboratories to analyze next-generation sequence data.
At the same time, the company announced that it is ending an existing agreement with the Broad Institute that authorized Appistry to sell a commercial version of the Broad's Genome Analysis Toolkit.
The newly-minted GenomePilot product features a user-friendly interface that provides access to preconfigured pipelines to identify actionable variants from raw sequence data from exome, whole genome, or gene panels, as well as data from tumor/normal and tumor-only cancer studies. Later iterations of the software will include a pre-configured pipeline for RNA-sequencing data.
Furthermore, the software offers access to multiple tool options for different tasks, for example, tools for variant calling include Pindel,SomaticSniper, and VarSeeker . Users can easily create custom pipelines that incorporate tools of their choice without having to worry about building or modifying scripts or using command line protocols.
Trevor Heritage, Appistry's vice president of sales and marketing, told GenomeWeb that the company developed GenomePilot to simplify the process of moving and implementing research-oriented informatics applications into the more regulated clinical and translational research laboratory environments.
By providing preconfigured pipelines and simple processes for creating custom pipelines that don't require in depth bioinformatics expertise, it bridges a gap that exists "between genomics research and some of the tools used there and what's really needed to make those tools effective for translational research and for clinical application," he said. It also frees researchers in these contexts to focus on address interesting scientific questions rather than optimizing pipelines for their projects, he said.
GenomePilot is available for local installation only with all software, tools, and data installed as a single package. Appistry charges an annual subscription fee that varies between $15,000 and $50,000 depending on the scale of the environment where the software is being deployed. The company is also partnering with Dell to provide a hardware/software bundle that will include a Dell workstation or server that will come pre-loaded with GenomePilot, Heritage said.
The bundled offering customers will have a choice of three or four standardized configuration options but if those choices aren't optimal, Dell and Appistry will work with the customer to create the IT environment best suited for their needs, Heritage said. However, the software can run on any hardware, so customers can simply purchase subscriptions to GenomePilot and install it on whatever local infrastructure they have, Heritage noted. The partners are still working through what the standard hardware configurations will be but they expect to flesh that out over the next several months, he said.
The launch of the software coincided with a second announcement that this month Appistry and the Broad Institute are ending an existing agreement that granted Appistry commercial licensing rights to the Broad's Genome Analysis Toolkit (GATK) and MuTect software solution.
The Broad first tapped St. Louis-based Appistry in 2012 to distribute and support a commercial version of the GATK to users at for-profit companies only — academics would continue to have free access through the Broad. The Broad had been mulling a commercial licensing scheme for the GATK so that it could offer more support to for-profit groups and as well to support future development of the tool.
At the time, David Altshuler, deputy director of the Broad Institute, told GenomeWeb that in selecting a commercialization partner, Broad also deemed it critical that its partner support the open source nature of the framework and that Broad would be able to give the tools to any academic, not-for-profit research user without any restriction or cost.
Since 2012, Appistry has provided a commercial version of GATK both as a standalone product and it also included the tool in its Cancer Genome Analysis suite (CGA), which is used for analyzing tumor next-generation sequencing data. The CGA also featured the Broad's MuTect — a tool for identifying somatic mutations in tumor/normal pairs that Appistry was authorized to provide commercially in 2013. Heritage told GenomeWeb that in the years since the agreement was signed, over 100 customers including large pharmaceutical companies, cancer centers, and academic institutions have licensed the commercial version of GATK and CGA.
But as of April 15, Appistry will begin a transition process to return commercial licensing options to the Broad Institute per the institution's request and contractual right, the company said. What that transition process will look like is still unclear at the moment but existing customers of the commercial solution will be fully supported with no disruptions to their systems until their licenses expire, Heritage said. The company also continue to provide access to the GATK and MuTect through its solutions, Heritage said. Both of these tools are among the options for use in analysis pipelines in the newly launched GenomePilot offering and MuTect is a core component of Appistry's CGA software. After April 15, commercial customers will need to have their own licenses to these tools in order to access them through GenomePilot.
After that date, commercial entities seeking access to the GATK or MuTect should contact the Broad Institute — which is now once again handling commercial licensing for both tools — for information on availability and licensing terms.
It's not entirely clear why the Broad chose not to keep its partnership with Appistry and the institute has not provided details about how it will handle commercial licenses for the GATK — details about pricing and commercial customer support are still being worked out. It has said in a post on the GATK blog that commercial customers will have an option to license GATK as a standalone package or as part of a second package that will bundle it with MuTect and the ContEst software.
The post also states that the new arrangement gives commercial customers "greater" access and contact with the GATK support team as well as access to the most current iterations of the GATK and best practice recommendations.
The Broad declined to provide additional comments to GenomeWeb about the end of its agreement with Appistry as well as its plans moving forward beyond what has already been posted on the GATK blog.